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- PDB-1d9g: BOVINE INTERFERON-GAMMA AT 2.9 ANGSTROMS -

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Basic information

Entry
Database: PDB / ID: 1d9g
TitleBOVINE INTERFERON-GAMMA AT 2.9 ANGSTROMS
ComponentsINTERFERON-GAMMA
KeywordsIMMUNE SYSTEM / helical homodimer
Function / homology
Function and homology information


Interferon gamma signaling / Regulation of IFNG signaling / IFNG signaling activates MAPKs / type II interferon receptor binding / humoral immune response / positive regulation of B cell proliferation / cytokine activity / defense response to virus / adaptive immune response / positive regulation of transcription by RNA polymerase II / extracellular space
Similarity search - Function
Interferon gamma / Interferon gamma / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsRandal, M. / Kossiakoff, A.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2000
Title: The 2.0 A structure of bovine interferon-gamma; assessment of the structural differences between species.
Authors: Randal, M. / Kossiakoff, A.A.
History
DepositionOct 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERFERON-GAMMA
B: INTERFERON-GAMMA


Theoretical massNumber of molelcules
Total (without water)28,5112
Polymers28,5112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-50 kcal/mol
Surface area12690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.600, 79.600, 82.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe asymmetric unit contains the biologically relevant homodimer

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Components

#1: Protein INTERFERON-GAMMA


Mass: 14255.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P07353

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MES, sodium chloride, ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 %satammonium sulfate1reservoir
24 mg/mlprotein1drop
350 mMMES1drop
40.5 M1dropNaCl

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 28, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→8 Å / Num. all: 6450 / Num. obs: 6450 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.75 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 26.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.26 / Num. unique all: 535 / % possible all: 87.7
Reflection shell
*PLUS
% possible obs: 87.7 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851refinement
XDSdata reduction
AUTOMARdata reduction
RefinementResolution: 2.9→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: NCS restraints were applied to individual helices
RfactorNum. reflection% reflectionSelection details
Rfree0.308 661 -random
Rwork0.218 ---
all0.229 6065 --
obs0.229 6065 97.1 %-
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 0 0 0 1940
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.33
X-RAY DIFFRACTIONx_bond_d0.009

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